Aerobically fit children outperform less fit peers on cognitive control challenges that involve inhibition, cognitive flexibility, and working memory. The aim of this study was to determine whether, compared with less fit children, more fit 9- and 10-year-old pre-adolescents exhibit superior performance on a modified compatible and incompatible flanker task of cognitive control at the initial time of fitness testing and approximately one year later. We found that more fit children demonstrated increased flanker accuracy at both test sessions, coupled with a superior ability to flexibly allocate strategies during task conditions that required different amounts of cognitive control, relative to less fit children. More fit children also gained a speed benefit at follow-up testing. Structural MRI data were also collected to investigate the relationship between basal ganglia volume and task performance. Bilateral putamen volumes of the dorsal striatum and globus pallidus volumes predicted flanker performance at initial and follow-up testing one year later. The present findings suggest that childhood aerobic fitness and basal ganglia volumes relate to cognitive control at the time of fitness testing and may play a role in cognitive performance in the future. We hope that this research will encourage public health and educational changes that will promote a physically active lifestyle in children.